mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NZ_CP022686 | 119,184 | T→G | 11.8% | F47V (TTT→GTT) | marB → | multiple antibiotic resistance protein MarB |
| RA | NZ_CP022686 | 340,516 | A→C | 12.4% | F31V (TTT→GTT) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 360,227 | T→G | 16.3% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 418,374 | T→G | 14.0% | F48V (TTT→GTT) | znuB → | zinc ABC transporter permease subunit ZnuB |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 512,717 | T→G | 19.6% | intergenic (‑217/+13) | sdiA ← / ← yecC | transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC |
| RA | NZ_CP022686 | 560,880 | C→T | 100% | intergenic (+62/+53) | CIW80_RS03085 → / ← pilV | hypothetical protein/shufflon system plasmid conjugative transfer pilus tip adhesin PilV |
| RA | NZ_CP022686 | 601,302 | T→G | 21.2% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 693,021 | A→C | 9.2% | T121P (ACG→CCG) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 694,406 | G→T | 18.9% | intergenic (+166/‑30) | CIW80_RS03555 → / → CIW80_RS03560 | transposase/PfkB family carbohydrate kinase |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 764,997 | T→G | 11.1% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,441 | C→A | 18.3% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 18.7% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 837,555 | T→G | 15.8% | intergenic (‑128/+95) | thiM ← / ← rcnR | hydroxyethylthiazole kinase/Ni(II)/Co(II)‑binding transcriptional repressor RcnR |
| RA | NZ_CP022686 | 917,427:1 | +TT | 100% | intergenic (+130/‑91) | yeiP → / → yeiQ | elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein |
| RA | NZ_CP022686 | 1,005,085 | C→A | 14.5% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,047,883 | T→G | 8.5% | intergenic (‑113/+51) | nuoM ← / ← nuoL | NADH‑quinone oxidoreductase subunit M/NADH‑quinone oxidoreductase subunit L |
| RA | NZ_CP022686 | 1,100,944 | T→G | 15.5% | D187A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,371,071 | G→T | 16.4% | D29Y (GAT→TAT) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,547,000 | G→C | 15.1% | intergenic (+22/‑12) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,564,569 | A→C | 13.3% | K190N (AAA→AAC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 12.4% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,640,888 | G→T | 18.9% | intergenic (+34/‑17) | ssnA → / → ygfM | putative aminohydrolase SsnA/molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,224 | T→G | 11.1% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,032 | G→T | 12.3% | intergenic (‑642/‑13) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,716,167 | A→C | 12.6% | N49T (AAC→ACC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,954,923 | T→G | 20.9% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 1,965,144 | C→G | 6.6% | R96P (CGC→CCC) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 2,011,244 | T→G | 9.4% | A53A (GCA→GCC) | tdcD ← | propionate kinase |
| RA | NZ_CP022686 | 2,049,089 | T→G | 12.3% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,148,115 | T→G | 14.0% | L126R (CTG→CGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 7.3% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,226,139 | A→C | 6.1% | D9A (GAC→GCC) | crp → | cAMP‑activated global transcriptional regulator CRP |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,357,284 | G→C | 13.5% | D24H (GAC→CAC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,394,287 | T→G | 24.1% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,394,295 | G→T | 10.2% | I112I (ATC→ATA) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,398,896 | A→C | 15.1% | K206N (AAA→AAC) | hutW → | heme anaerobic degradation radical SAM methyltransferase ChuW/HutW |
| RA | NZ_CP022686 | 2,406,338 | A→C | 7.6% | V62V (GTT→GTG) | CIW80_RS12130 ← | hypothetical protein |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,460,581 | A→C | 31.3% | intergenic (‑3/‑155) | yhjY ← / → tag | autotransporter outer membrane beta‑barrel domain‑containing protein/DNA‑3‑methyladenine glycosylase I |
| RA | NZ_CP022686 | 2,470,422 | T→G | 10.1% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,736,578 | C→A | 8.2% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,563 | T→G | 12.3% | noncoding (65/87 nt) | CIW80_RS13750 → | tRNA‑Leu |
| RA | NZ_CP022686 | 2,758,128 | A→C | 11.7% | K40N (AAA→AAC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,758,144 | A→C | 11.9% | T46P (ACG→CCG) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,868,740 | T→G | 25.0% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 17.5% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,929,407 | T→G | 5.5% | K787N (AAA→AAC) | ptsP ← | phosphoenolpyruvate‑‑protein phosphotransferase |
| RA | NZ_CP022686 | 2,974,930 | A→C | 12.7% | D124A (GAC→GCC) | rplJ → | 50S ribosomal protein L10 |
| RA | NZ_CP022686 | 2,989,627 | T→G | 10.6% | Q39H (CAA→CAC) | thiC ← | phosphomethylpyrimidine synthase ThiC |
| RA | NZ_CP022686 | 3,020,229 | T→G | 14.2% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,252,190 | T→G | 23.7% | K221N (AAA→AAC) | CIW80_RS16225 ← | enoyl‑CoA hydratase/isomerase family protein |
| RA | NZ_CP022686 | 3,287,019 | A→C | 13.4% | E108D (GAA→GAC) | cybC → | cytochrome b562 |
| RA | NZ_CP022686 | 3,297,360 | T→G | 10.6% | L837V (TTA→GTA) | mgtA → | magnesium‑translocating P‑type ATPase |
| RA | NZ_CP022686 | 3,390,604 | C→G | 16.0% | D147H (GAC→CAC) | sgcX ← | M42 family metallopeptidase |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,215 | A→T | 14.2% | intergenic (‑24/+11) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 19.5% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,247 | A→C | 20.3% | noncoding (66/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,574,983 | C→A | 7.0% | L184F (TTG→TTT) | sgrR ← | DNA‑binding transcriptional regulator SgrR |
| RA | NZ_CP022686 | 3,604,564 | G→T | 13.8% | intergenic (+80/‑151) | lpxC → / → secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/secA translation cis‑regulator SecM |
| RA | NZ_CP022686 | 3,652,079 | T→G | 11.5% | intergenic (‑88/+24) | panB ← / ← CIW80_RS18255 | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,734,367 | T→G | 18.0% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,806,228 | T→A | 8.4% | N1573K (AAT→AAA) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| RA | NZ_CP022686 | 3,818,252 | G→C | 7.2% | D312E (GAC→GAG) | pic ← | serine protease autotransporter toxin Pic |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,928,345 | T→G | 11.9% | F277V (TTC→GTC) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,940,724 | A→C | 11.9% | V308G (GTA→GGA) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 13.8% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 3,977,656 | A→C | 9.8% | K88N (AAA→AAC) | phoR → | phosphate regulon sensor histidine kinase PhoR |
| RA | NZ_CP022686 | 3,981,933 | T→G | 13.2% | intergenic (+70/‑86) | proY → / → malZ | proline‑specific permease ProY/maltodextrin glucosidase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 13.8% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,056,962 | C→A | 19.0% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,368,341 | T→G | 12.3% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,324 | C→A | 15.8% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,571,417 | T→G | 10.5% | A66A (GCA→GCC) | pgaC ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase |
| RA | NZ_CP022686 | 4,632,182 | T→G | 8.0% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,678,041 | A→C | 25.5% | intergenic (+39/‑82) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,804,059 | A→C | 11.2% | E620A (GAG→GCG) | CIW80_RS24225 → | phage terminase large subunit family protein |
| RA | NZ_CP022686 | 4,807,491 | G→T | 5.3% | G18C (GGT→TGT) | CIW80_RS24245 → | head decoration protein |
| RA | NZ_CP022686 | 4,814,961 | T→G | 14.5% | F61C (TTT→TGT) | CIW80_RS24295 → | phage tail protein |
| MC JC | NZ_CP022686 | 4,844,868 | Δ1,662 bp | 100% | [umuD]–[umuC] | [umuD], [umuC] | |
| RA | NZ_CP022686 | 4,870,912 | Δ1 bp | 100% | intergenic (‑108/‑120) | dhaK ← / → dhaR | dihydroxyacetone kinase subunit DhaK/dihydroxyacetone kinase operon transcriptional regulator DhaR |
| RA | NZ_CP022686 | 5,001,157 | G→T | 14.1% | D161Y (GAT→TAT) | ompG → | monomeric porin OmpG |
| RA | NZ_CP022686 | 5,042,151 | T→C | 6.9% | V594V (GTT→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,648 | G→C | 5.9% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,215 | T→G | 13.6% | N1282K (AAT→AAG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 2,031 | G→A | 100% | intergenic (‑235/‑1500) | putative rom (RNA I inhibition modulator protein) ← / → ompA | –/– |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,595 | Δ15 bp | 100% | [IL2wt no signal] | [IL2wt no signal] | |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,019 | +CAT | 7.7% | intergenic (+12/+37) | IL2wt no signal → / ← annotated as hok_sok locus | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 654–2618 | 3068–2957 | 340–2415 | 7165 [6933] | [6427] 7195 | JNG15_RS00010–mobA | JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMut‑Ompa‑D5‑IL2wt‑His6 | 4746–4877 | 5478–5214 | 338–733 | 3990 [3811] | [0] NA | [putative HTH domain protein] | [putative HTH domain protein] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 1 (0.010) | 135 (0.910) | 60/248 | NT | 99.3% | coding (320/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1524130 | NA (NA) | intergenic (+8/+232) | CIW80_RS07590/syd | IS3‑like element ISEc52 family transposase/SecY‑interacting protein | |||||
| * | ? | NZ_CP022686 | = 262468 | 1 (0.010) | 131 (0.880) | 56/248 | NT | 99.2% | coding (322/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1761697 | NA (NA) | intergenic (‑72/‑70) | CIW80_RS08710/CIW80_RS08720 | IS3‑like element ISEc52 family transposase/IS3‑like element IS600 family transposase | |||||
| * | ? | NZ_CP022686 | 1522881 = | NA (NA) | 7111 (2.160) | 224/248 | NT | 98.0% | intergenic (‑394/‑72) | yqcC/CIW80_RS07590 | YqcC family protein/IS3‑like element ISEc52 family transposase |
| ? | pMut‑Ompa‑D5‑IL2wt‑His6 | 3853 = | 143 (0.020) | coding (245/399 nt) | IL2wt no signal | ||||||
| * | ? | NZ_CP022686 | = 1524127 | NA (NA) | 7446 (2.320) | 224/242 | NT | 97.7% | intergenic (+5/+235) | CIW80_RS07590/syd | IS3‑like element ISEc52 family transposase/SecY‑interacting protein |
| ? | pMut‑Ompa‑D5‑IL2wt‑His6 | = 3859 | 180 (0.030) | coding (251/399 nt) | IL2wt no signal | ||||||
| * | ? | NZ_CP022686 | 4514374 = | 137 (0.920) | 7 (0.000) +AGCT |
6/240 | NT | 9.1% | coding (59/1053 nt) | ompA | porin OmpA |
| ? | pMut‑Ompa‑D5‑IL2wt‑His6 | 3609 = | 7 (0.000) | coding (1/399 nt) | IL2wt no signal | ||||||